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(-) Description

Title :  CRYSTAL STRUCTURE OF RCL WITH 5'-PHIOSPHOROTHIOATE-ADENOSINE
 
Authors :  G. Labesse, A. Padilla, P. A. Kaminski
Date :  04 Jul 12  (Deposition) - 02 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Deoxyribonucleoside 5'-Monophosphate N-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Padilla, C. Amiable, S. Pochet, P. A. Kaminski, G. Labesse
Structure Of The Oncoprotein Rcl Bound To Three Nucleotide Analogues.
Acta Crystallogr. , Sect. D V. 69 247 2013
PubMed-ID: 23385460  |  Reference-DOI: 10.1107/S0907444912045039

(-) Compounds

Molecule 1 - DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 11-151
    Gene: RCL
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: C-MYC-RESPONSIVE PROTEIN RCL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2SRA4Ligand/IonADENOSINE -5'-THIO-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2SRA2Ligand/IonADENOSINE -5'-THIO-MONOPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2SRA2Ligand/IonADENOSINE -5'-THIO-MONOPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , GLY A:16 , ILE A:18 , ARG A:19 , GLY A:20 , GLU A:44 , ILE A:65 , ASN A:69 , SER A:87 , GLY A:89 , GLU A:93 , HOH A:309 , HOH A:315 , HOH A:423 , HOH A:457 , SER B:117 , ALA B:118 , MET B:119BINDING SITE FOR RESIDUE SRA A 201
2AC2SOFTWAREARG A:37 , SER B:33 , ARG B:36BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARESER A:117 , ALA A:118 , MET A:119 , CYS B:15 , GLY B:16 , ILE B:18 , ARG B:19 , GLY B:20 , ILE B:65 , ASN B:69 , SER B:87 , GLY B:89 , GLU B:93 , HOH B:302 , HOH B:331 , HOH B:376 , HOH B:439BINDING SITE FOR RESIDUE SRA B 201
4AC4SOFTWARESER A:33 , ARG B:34 , ARG B:37BINDING SITE FOR RESIDUE SO4 B 202
5AC5SOFTWARECYS C:15 , GLY C:16 , ILE C:18 , ARG C:19 , GLY C:20 , ILE C:65 , ASN C:69 , SER C:87 , GLY C:89 , VAL C:90 , GLU C:93 , HOH C:303 , HOH C:324 , HOH C:325 , HOH C:395 , HOH C:405 , SER D:117 , ALA D:118 , MET D:119BINDING SITE FOR RESIDUE SRA C 201
6AC6SOFTWARESER C:117 , ALA C:118 , MET C:119 , CYS D:15 , GLY D:16 , ILE D:18 , ARG D:19 , GLY D:20 , ILE D:65 , ASN D:69 , SER D:87 , GLY D:89 , GLU D:93 , HOH D:302 , HOH D:319 , HOH D:344 , HOH D:394BINDING SITE FOR RESIDUE SRA D 201
7AC7SOFTWARESER C:33 , ARG C:36 , ARG D:34 , ARG D:37BINDING SITE FOR RESIDUE SO4 D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FYK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FYK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FYK)

(-) Exons   (0, 0)

(no "Exon" information available for 4FYK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhh....eeeee....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fyk A  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFE 148
                                    19        29        39     || 62        72        82        92       102       112       122       132       142      
                                                              45|                                                                                         
                                                               59                                                                                         


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhhhh....eeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyk B  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    19        29        39   ||   66        76        86        96       106       116       126       136       146    
                                                            43|                                                                                         
                                                             61                                                                                         


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhh....eeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyk C  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFE 148
                                    19        29        39    ||  63        73        83        93       103       113       123       133       143     
                                                             44|                                                                                         
                                                              59                                                                                         


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhh....eeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyk D  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAL 150
                                    19        29        39   ||   66        76        86        96       106       116       126       136       146    
                                                            43|                                                                                         
                                                             61
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4FYK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FYK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FYK)

(-) Gene Ontology  (15, 15)

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        DNPH1_RAT | O35820: 2khz 2klh 4fyh 4fyi 4kxl 4kxm 4kxn 4p5d

(-) Related Entries Specified in the PDB File

4fyh 4fyi